2024-04-03T11:28:01,520 Created temporary directory: /tmp/pip-build-tracker-iuyc3gh2 2024-04-03T11:28:01,521 Initialized build tracking at /tmp/pip-build-tracker-iuyc3gh2 2024-04-03T11:28:01,522 Created build tracker: /tmp/pip-build-tracker-iuyc3gh2 2024-04-03T11:28:01,522 Entered build tracker: /tmp/pip-build-tracker-iuyc3gh2 2024-04-03T11:28:01,523 Created temporary directory: /tmp/pip-wheel-rk0t09ws 2024-04-03T11:28:01,526 Created temporary directory: /tmp/pip-ephem-wheel-cache-k9e6tgnd 2024-04-03T11:28:01,548 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-03T11:28:01,552 2 location(s) to search for versions of ont-spectre: 2024-04-03T11:28:01,552 * https://pypi.org/simple/ont-spectre/ 2024-04-03T11:28:01,552 * https://www.piwheels.org/simple/ont-spectre/ 2024-04-03T11:28:01,552 Fetching project page and analyzing links: https://pypi.org/simple/ont-spectre/ 2024-04-03T11:28:01,553 Getting page https://pypi.org/simple/ont-spectre/ 2024-04-03T11:28:01,555 Found index url https://pypi.org/simple/ 2024-04-03T11:28:01,768 Fetched page https://pypi.org/simple/ont-spectre/ as application/vnd.pypi.simple.v1+json 2024-04-03T11:28:01,769 Found link https://files.pythonhosted.org/packages/8c/ac/f5d215a7de78360886138cac41885b9b109419966ec8a9e6ffeb26c08391/ont-spectre-0.2.0.tar.gz (from https://pypi.org/simple/ont-spectre/), version: 0.2.0 2024-04-03T11:28:01,770 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-spectre/ 2024-04-03T11:28:01,770 Getting page https://www.piwheels.org/simple/ont-spectre/ 2024-04-03T11:28:01,771 Found index url https://www.piwheels.org/simple/ 2024-04-03T11:28:02,119 Fetched page https://www.piwheels.org/simple/ont-spectre/ as text/html 2024-04-03T11:28:02,121 Skipping link: not a file: https://www.piwheels.org/simple/ont-spectre/ 2024-04-03T11:28:02,121 Skipping link: not a file: https://pypi.org/simple/ont-spectre/ 2024-04-03T11:28:02,148 Given no hashes to check 1 links for project 'ont-spectre': discarding no candidates 2024-04-03T11:28:02,174 Collecting ont-spectre==0.2.0 2024-04-03T11:28:02,178 Created temporary directory: /tmp/pip-unpack-r4ueda5c 2024-04-03T11:28:02,470 Downloading ont-spectre-0.2.0.tar.gz (96 kB) 2024-04-03T11:28:02,629 Added ont-spectre==0.2.0 from https://files.pythonhosted.org/packages/8c/ac/f5d215a7de78360886138cac41885b9b109419966ec8a9e6ffeb26c08391/ont-spectre-0.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-iuyc3gh2' 2024-04-03T11:28:02,631 Running setup.py (path:/tmp/pip-wheel-rk0t09ws/ont-spectre_377db9dd739345598454de3fa54a417f/setup.py) egg_info for package ont-spectre 2024-04-03T11:28:02,632 Created temporary directory: /tmp/pip-pip-egg-info-89bkranp 2024-04-03T11:28:02,632 Preparing metadata (setup.py): started 2024-04-03T11:28:02,634 Running command python setup.py egg_info 2024-04-03T11:28:03,086 /tmp/pip-wheel-rk0t09ws/ont-spectre_377db9dd739345598454de3fa54a417f/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-03T11:28:03,086 import pkg_resources 2024-04-03T11:28:03,661 running egg_info 2024-04-03T11:28:03,662 creating /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info 2024-04-03T11:28:03,687 writing /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/PKG-INFO 2024-04-03T11:28:03,691 writing dependency_links to /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/dependency_links.txt 2024-04-03T11:28:03,692 writing entry points to /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/entry_points.txt 2024-04-03T11:28:03,694 writing requirements to /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/requires.txt 2024-04-03T11:28:03,695 writing top-level names to /tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/top_level.txt 2024-04-03T11:28:03,696 writing manifest file '/tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/SOURCES.txt' 2024-04-03T11:28:03,781 reading manifest file '/tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/SOURCES.txt' 2024-04-03T11:28:03,782 reading manifest template 'MANIFEST.in' 2024-04-03T11:28:03,784 adding license file 'LICENSE.md' 2024-04-03T11:28:03,786 writing manifest file '/tmp/pip-pip-egg-info-89bkranp/ont_spectre.egg-info/SOURCES.txt' 2024-04-03T11:28:03,895 Preparing metadata (setup.py): finished with status 'done' 2024-04-03T11:28:03,899 Source in /tmp/pip-wheel-rk0t09ws/ont-spectre_377db9dd739345598454de3fa54a417f has version 0.2.0, which satisfies requirement ont-spectre==0.2.0 from https://files.pythonhosted.org/packages/8c/ac/f5d215a7de78360886138cac41885b9b109419966ec8a9e6ffeb26c08391/ont-spectre-0.2.0.tar.gz 2024-04-03T11:28:03,900 Removed ont-spectre==0.2.0 from https://files.pythonhosted.org/packages/8c/ac/f5d215a7de78360886138cac41885b9b109419966ec8a9e6ffeb26c08391/ont-spectre-0.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-iuyc3gh2' 2024-04-03T11:28:03,904 Created temporary directory: /tmp/pip-unpack-3w26y0e4 2024-04-03T11:28:03,905 Created temporary directory: /tmp/pip-unpack-2q13ud4b 2024-04-03T11:28:03,915 Building wheels for collected packages: ont-spectre 2024-04-03T11:28:03,919 Created temporary directory: /tmp/pip-wheel-3_2d0ke5 2024-04-03T11:28:03,919 Building wheel for ont-spectre (setup.py): started 2024-04-03T11:28:03,921 Destination directory: /tmp/pip-wheel-3_2d0ke5 2024-04-03T11:28:03,921 Running command python setup.py bdist_wheel 2024-04-03T11:28:04,376 /tmp/pip-wheel-rk0t09ws/ont-spectre_377db9dd739345598454de3fa54a417f/setup.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2024-04-03T11:28:04,376 import pkg_resources 2024-04-03T11:28:04,947 running bdist_wheel 2024-04-03T11:28:05,046 running build 2024-04-03T11:28:05,047 running build_py 2024-04-03T11:28:05,074 creating build 2024-04-03T11:28:05,075 creating build/lib 2024-04-03T11:28:05,075 creating build/lib/spectre 2024-04-03T11:28:05,076 copying spectre/spectreCNVPopulation.py -> build/lib/spectre 2024-04-03T11:28:05,079 copying spectre/__init__.py -> build/lib/spectre 2024-04-03T11:28:05,081 copying spectre/spectreCNV.py -> build/lib/spectre 2024-04-03T11:28:05,083 copying spectre/main.py -> build/lib/spectre 2024-04-03T11:28:05,086 creating build/lib/spectre/analysis 2024-04-03T11:28:05,087 copying spectre/analysis/cnv_metrics.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,090 copying spectre/analysis/coverage_stats.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,091 copying spectre/analysis/cnv_candidate.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,093 copying spectre/analysis/__init__.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,095 copying spectre/analysis/call_cnv_AF.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,097 copying spectre/analysis/analysis.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,099 copying spectre/analysis/call_cnv_coverage.py -> build/lib/spectre/analysis 2024-04-03T11:28:05,102 creating build/lib/spectre/util 2024-04-03T11:28:05,103 copying spectre/util/mosdepthReader.py -> build/lib/spectre/util 2024-04-03T11:28:05,105 copying spectre/util/outputWriter.py -> build/lib/spectre/util 2024-04-03T11:28:05,107 copying spectre/util/cnv_id.py -> build/lib/spectre/util 2024-04-03T11:28:05,109 copying spectre/util/__init__.py -> build/lib/spectre/util 2024-04-03T11:28:05,110 copying spectre/util/OSUtil.py -> build/lib/spectre/util 2024-04-03T11:28:05,112 copying spectre/util/dataAnalyzer.py -> build/lib/spectre/util 2024-04-03T11:28:05,113 copying spectre/util/vcf_parser.py -> build/lib/spectre/util 2024-04-03T11:28:05,116 creating build/lib/spectre/plots 2024-04-03T11:28:05,117 copying spectre/plots/__init__.py -> build/lib/spectre/plots 2024-04-03T11:28:05,119 copying spectre/plots/plot.py -> build/lib/spectre/plots 2024-04-03T11:28:05,121 creating build/lib/spectre/util/metadata 2024-04-03T11:28:05,122 copying spectre/util/metadata/metadataCollector.py -> build/lib/spectre/util/metadata 2024-04-03T11:28:05,124 copying spectre/util/metadata/__init__.py -> build/lib/spectre/util/metadata 2024-04-03T11:28:05,129 creating build/lib/spectre/data 2024-04-03T11:28:05,130 copying spectre/data/grch37_blacklist_normal.bed -> build/lib/spectre/data 2024-04-03T11:28:05,132 copying spectre/data/black_list_bins_0.01_merged.bed -> build/lib/spectre/data 2024-04-03T11:28:05,135 copying spectre/data/black_list_bins_0.02_merged.bed -> build/lib/spectre/data 2024-04-03T11:28:05,137 copying spectre/data/grch37_blacklist_spectre.bed -> build/lib/spectre/data 2024-04-03T11:28:05,139 copying spectre/data/grch38_blacklist.bed -> build/lib/spectre/data 2024-04-03T11:28:05,142 copying spectre/data/black_list_bins_0.03_merged.bed -> build/lib/spectre/data 2024-04-03T11:28:05,145 copying spectre/data/grch37_blacklist_plus.bed -> build/lib/spectre/data 2024-04-03T11:28:05,147 copying spectre/data/grch38_y.txt -> build/lib/spectre/data 2024-04-03T11:28:05,149 copying spectre/data/metadata_GRCh38_no_alt.mdr -> build/lib/spectre/data 2024-04-03T11:28:05,179 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-03T11:28:05,180 !! 2024-04-03T11:28:05,181 ******************************************************************************** 2024-04-03T11:28:05,181 Please avoid running ``setup.py`` directly. 2024-04-03T11:28:05,182 Instead, use pypa/build, pypa/installer or other 2024-04-03T11:28:05,182 standards-based tools. 2024-04-03T11:28:05,183 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-03T11:28:05,184 ******************************************************************************** 2024-04-03T11:28:05,185 !! 2024-04-03T11:28:05,185 self.initialize_options() 2024-04-03T11:28:05,206 installing to build/bdist.linux-armv7l/wheel 2024-04-03T11:28:05,207 running install 2024-04-03T11:28:05,231 running install_lib 2024-04-03T11:28:05,256 creating build/bdist.linux-armv7l 2024-04-03T11:28:05,257 creating build/bdist.linux-armv7l/wheel 2024-04-03T11:28:05,259 creating build/bdist.linux-armv7l/wheel/spectre 2024-04-03T11:28:05,260 creating build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,261 copying build/lib/spectre/data/grch37_blacklist_normal.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,263 copying build/lib/spectre/data/black_list_bins_0.01_merged.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,266 copying build/lib/spectre/data/black_list_bins_0.02_merged.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,269 copying build/lib/spectre/data/grch37_blacklist_spectre.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,271 copying build/lib/spectre/data/grch38_blacklist.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,273 copying build/lib/spectre/data/black_list_bins_0.03_merged.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,276 copying build/lib/spectre/data/grch37_blacklist_plus.bed -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,278 copying build/lib/spectre/data/grch38_y.txt -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,279 copying build/lib/spectre/data/metadata_GRCh38_no_alt.mdr -> build/bdist.linux-armv7l/wheel/spectre/data 2024-04-03T11:28:05,283 creating build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,284 copying build/lib/spectre/analysis/cnv_metrics.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,286 copying build/lib/spectre/analysis/coverage_stats.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,288 copying build/lib/spectre/analysis/cnv_candidate.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,290 copying build/lib/spectre/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,292 copying build/lib/spectre/analysis/call_cnv_AF.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,294 copying build/lib/spectre/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,297 copying build/lib/spectre/analysis/call_cnv_coverage.py -> build/bdist.linux-armv7l/wheel/spectre/analysis 2024-04-03T11:28:05,299 copying build/lib/spectre/spectreCNVPopulation.py -> build/bdist.linux-armv7l/wheel/spectre 2024-04-03T11:28:05,302 creating build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,303 creating build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-04-03T11:28:05,304 copying build/lib/spectre/util/metadata/metadataCollector.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-04-03T11:28:05,306 copying build/lib/spectre/util/metadata/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util/metadata 2024-04-03T11:28:05,308 copying build/lib/spectre/util/mosdepthReader.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,309 copying build/lib/spectre/util/outputWriter.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,312 copying build/lib/spectre/util/cnv_id.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,313 copying build/lib/spectre/util/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,315 copying build/lib/spectre/util/OSUtil.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,317 copying build/lib/spectre/util/dataAnalyzer.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,318 copying build/lib/spectre/util/vcf_parser.py -> build/bdist.linux-armv7l/wheel/spectre/util 2024-04-03T11:28:05,321 copying build/lib/spectre/__init__.py -> build/bdist.linux-armv7l/wheel/spectre 2024-04-03T11:28:05,322 copying build/lib/spectre/spectreCNV.py -> build/bdist.linux-armv7l/wheel/spectre 2024-04-03T11:28:05,324 copying build/lib/spectre/main.py -> build/bdist.linux-armv7l/wheel/spectre 2024-04-03T11:28:05,327 creating build/bdist.linux-armv7l/wheel/spectre/plots 2024-04-03T11:28:05,328 copying build/lib/spectre/plots/__init__.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-04-03T11:28:05,330 copying build/lib/spectre/plots/plot.py -> build/bdist.linux-armv7l/wheel/spectre/plots 2024-04-03T11:28:05,331 running install_egg_info 2024-04-03T11:28:05,394 running egg_info 2024-04-03T11:28:05,418 writing ont_spectre.egg-info/PKG-INFO 2024-04-03T11:28:05,421 writing dependency_links to ont_spectre.egg-info/dependency_links.txt 2024-04-03T11:28:05,422 writing entry points to ont_spectre.egg-info/entry_points.txt 2024-04-03T11:28:05,424 writing requirements to ont_spectre.egg-info/requires.txt 2024-04-03T11:28:05,425 writing top-level names to ont_spectre.egg-info/top_level.txt 2024-04-03T11:28:05,456 reading manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-04-03T11:28:05,459 reading manifest template 'MANIFEST.in' 2024-04-03T11:28:05,460 adding license file 'LICENSE.md' 2024-04-03T11:28:05,463 writing manifest file 'ont_spectre.egg-info/SOURCES.txt' 2024-04-03T11:28:05,464 Copying ont_spectre.egg-info to build/bdist.linux-armv7l/wheel/ont_spectre-0.2.0-py3.11.egg-info 2024-04-03T11:28:05,476 running install_scripts 2024-04-03T11:28:05,492 creating build/bdist.linux-armv7l/wheel/ont_spectre-0.2.0.dist-info/WHEEL 2024-04-03T11:28:05,494 creating '/tmp/pip-wheel-3_2d0ke5/ont_spectre-0.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-03T11:28:05,497 adding 'spectre/__init__.py' 2024-04-03T11:28:05,500 adding 'spectre/main.py' 2024-04-03T11:28:05,502 adding 'spectre/spectreCNV.py' 2024-04-03T11:28:05,504 adding 'spectre/spectreCNVPopulation.py' 2024-04-03T11:28:05,507 adding 'spectre/analysis/__init__.py' 2024-04-03T11:28:05,511 adding 'spectre/analysis/analysis.py' 2024-04-03T11:28:05,513 adding 'spectre/analysis/call_cnv_AF.py' 2024-04-03T11:28:05,515 adding 'spectre/analysis/call_cnv_coverage.py' 2024-04-03T11:28:05,516 adding 'spectre/analysis/cnv_candidate.py' 2024-04-03T11:28:05,519 adding 'spectre/analysis/cnv_metrics.py' 2024-04-03T11:28:05,520 adding 'spectre/analysis/coverage_stats.py' 2024-04-03T11:28:05,530 adding 'spectre/data/black_list_bins_0.01_merged.bed' 2024-04-03T11:28:05,537 adding 'spectre/data/black_list_bins_0.02_merged.bed' 2024-04-03T11:28:05,549 adding 'spectre/data/black_list_bins_0.03_merged.bed' 2024-04-03T11:28:05,550 adding 'spectre/data/grch37_blacklist_normal.bed' 2024-04-03T11:28:05,552 adding 'spectre/data/grch37_blacklist_plus.bed' 2024-04-03T11:28:05,553 adding 'spectre/data/grch37_blacklist_spectre.bed' 2024-04-03T11:28:05,554 adding 'spectre/data/grch38_blacklist.bed' 2024-04-03T11:28:05,555 adding 'spectre/data/grch38_y.txt' 2024-04-03T11:28:05,559 adding 'spectre/data/metadata_GRCh38_no_alt.mdr' 2024-04-03T11:28:05,561 adding 'spectre/plots/__init__.py' 2024-04-03T11:28:05,562 adding 'spectre/plots/plot.py' 2024-04-03T11:28:05,564 adding 'spectre/util/OSUtil.py' 2024-04-03T11:28:05,565 adding 'spectre/util/__init__.py' 2024-04-03T11:28:05,566 adding 'spectre/util/cnv_id.py' 2024-04-03T11:28:05,567 adding 'spectre/util/dataAnalyzer.py' 2024-04-03T11:28:05,569 adding 'spectre/util/mosdepthReader.py' 2024-04-03T11:28:05,570 adding 'spectre/util/outputWriter.py' 2024-04-03T11:28:05,572 adding 'spectre/util/vcf_parser.py' 2024-04-03T11:28:05,574 adding 'spectre/util/metadata/__init__.py' 2024-04-03T11:28:05,575 adding 'spectre/util/metadata/metadataCollector.py' 2024-04-03T11:28:05,577 adding 'ont_spectre-0.2.0.dist-info/LICENSE.md' 2024-04-03T11:28:05,579 adding 'ont_spectre-0.2.0.dist-info/METADATA' 2024-04-03T11:28:05,580 adding 'ont_spectre-0.2.0.dist-info/WHEEL' 2024-04-03T11:28:05,581 adding 'ont_spectre-0.2.0.dist-info/entry_points.txt' 2024-04-03T11:28:05,581 adding 'ont_spectre-0.2.0.dist-info/top_level.txt' 2024-04-03T11:28:05,582 adding 'ont_spectre-0.2.0.dist-info/RECORD' 2024-04-03T11:28:05,585 removing build/bdist.linux-armv7l/wheel 2024-04-03T11:28:05,706 Building wheel for ont-spectre (setup.py): finished with status 'done' 2024-04-03T11:28:05,709 Created wheel for ont-spectre: filename=ont_spectre-0.2.0-py3-none-any.whl size=103741 sha256=d0ee20985f63f04aeadc55e4657c01a6e65d21eee01ff8ac84abb42bebd14141 2024-04-03T11:28:05,711 Stored in directory: /tmp/pip-ephem-wheel-cache-k9e6tgnd/wheels/7a/5d/aa/2e018dc6f30729ae1c9903be489a7592c7d97fbe7ae013dca7 2024-04-03T11:28:05,722 Successfully built ont-spectre 2024-04-03T11:28:05,729 Removed build tracker: '/tmp/pip-build-tracker-iuyc3gh2'